Genome properties of key oil palm (Elaeis guineensis Jacq.) breeding populations - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement Access content directly
Journal Articles Journal of Applied Genetics Year : 2022

Genome properties of key oil palm (Elaeis guineensis Jacq.) breeding populations

Abstract

A good knowledge of the genome properties of the populations makes it possible to optimize breeding methods, in particular genomic selection (GS). In oil palm (Elaeis guineensis Jacq), the world's main source of vegetable oil, this would provide insight into the promising GS results obtained so far. The present study considered two complex breeding populations, Deli and La Me, with 943 individuals and 7324 single-nucleotide polymorphisms (SNPs) from genotyping-by-sequencing. Linkage disequilibrium (LD), haplotype sharing, effective size (N-e), and fixation index (F-st) were investigated. A genetic linkage map spanning 1778.52 cM and with a recombination rate of 2.85 cM/Mbp was constructed. The LD at r(2)=0.3, considered the minimum to get reliable GS results, spanned over 1.05 cM/0.22 Mbp in Deli and 0.9 cM/0.21 Mbp in La Me. The significant degree of differentiation existing between Deli and La Me was confirmed by the high F-st value (0.53), the pattern of correlation of SNP heterozygosity and allele frequency among populations, and the decrease of persistence of LD and of haplotype sharing among populations with increasing SNP distance. However, the level of resemblance between the two populations over short genomic distances (correlation of r values between populations >0.6 for SNPs separated by 40% for haplotypes <3600 bp/0.20 cM) likely explains the superiority of GS models ignoring the parental origin of marker alleles over models taking this information into account. The two populations had low N-e (<5). Population-specific genetic maps and reference genomes are recommended for future studies.
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hal-03703155 , version 1 (24-11-2023)

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Essubalew Getachew Seyum, Ngalle Hermine Bille, Wosene Gebreselassie Abtew, Pasi Rastas, Deni Arifianto, et al.. Genome properties of key oil palm (Elaeis guineensis Jacq.) breeding populations. Journal of Applied Genetics, 2022, ⟨10.1007/s13353-022-00708-w⟩. ⟨hal-03703155⟩
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